Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Table 1 Comparison of alternatively parameterized models of evolution in Fig. 1 indicates no significant difference in the Ka/Ks ratio at an early and a later stage of duplicate gene evolution.

Comparison	# base pairs	-lnL Ho	-lnL Ha	P value	Ka/Ks combined early and late	Ka/Ks ratio early	Ka/Ks ratio late	Ka/Ks diploid
Fig. 1B	80856	-165602.720	-165602.386	0.414	0.164	0.158	0.169	0.126
Fig. 1C	9717	-15699.366	-15697.250	1.000	0.208	0.124	0.346	0.198
Fig. 1D	6966	-13187.865	-13186.872	0.160	0.126	0.187	0.105	NA
Fig. 1B (partitioned)	80856	-160085.863	-159889.926	1.000	NL	Af2	Af2	NL
Fig. 1C (partitioned)	9717	-15400.349	-15393.089	0.888	NL	Af2	Af2	NL
Fig. 1D (partitioned)	6966	-12983.343	-12978.034	0.807	NL	Af2	Af2	NA

Indicated for comparisons depicted in Fig. 1B, C and D are likelihoods of the null model (early and later Ka/Ks are the same) and the alternative model (early and later Ka/Ks are not the same), the one-sided probability of the Ka/Ks ratio being higher in the early stage, and the Ka/Ks ratios estimated from each of these models. For the first two tests, the Ka/Ks ratio of the diploid lineage was estimated using a different model where a unique Ka/Ks ratio was estimated for each branch (a free ratio model). Also listed are the joint likelihoods of these models from an analysis partitioned by gene fragment. For the partitioned analyses, Ka/Ks ratios for each fragment are either listed in Additional file 2 (Af2), not listed (NL), or not applicable (NA).

ISSN: 2730-7182